ArticleJournal of molecular recognition : JMR
Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors.
Article in Journal of molecular recognition : JMR. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Discovery of novel dihydro-pyrimidine hybrids: insight into the design, synthesis, biological evaluation and absorption, distribution, metabolism and excretion studies.Future medicinal chemistry · 2024Article
- Article
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Site-directed mutations of anti-amantadine scFv antibody by molecular dynamics simulation: prediction and validation.Journal of molecular modeling · 2020Article
- Interleukin-6 increases matrix metalloproteinase-14 (MMP-14) levels via down-regulation of p53 to drive cancer progression.Oncotarget · 2016Article
- MDA-9/syntenin is essential for factor VIIa-induced signaling, migration, and metastasis in melanoma cells.The Journal of biological chemistry · 2015Article
- Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential.Journal of chemical theory and computation · 2012Article
- An integrated computational approach to rationalize the activity of non-zinc-binding MMP-2 inhibitors.PloS one · 2012Article
- Structural model of ligand-G protein-coupled receptor (GPCR) complex based on experimental double mutant cycle data: MT7 snake toxin bound to dimeric hM1 muscarinic receptor.The Journal of biological chemistry · 2011Article
- Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling.Journal of computer-aided molecular design · 2011Article
- POVME: an algorithm for measuring binding-pocket volumes.Journal of molecular graphics & modelling · 2011Article
- Molecular recognition in the case of flexible targets.Current pharmaceutical design · 2011Article
- Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach.Chemical biology & drug design · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
Matrix metalloproteinases (MMPs) comprise a class of flexible proteins required for normal tissue remodeling. Overexpression of MMPs is associated with a wide range of pathophysiological processes, including vascular disease, multiple sclerosis, Alzheimer's disease, and cancer. Nearly all MMP inhibitors have failed in clinical trials, in part due to lack of specificity. Due to the highly dynamic molecular motions of the MMP-2 binding pockets, the rational drug design of MMP inhibitors has been very challenging. To address these challenges, in the current study we combine computer docking with molecular dynamics (MD) simulations in order to incorporate receptor-flexibility and induced-fit effects into the drug-design process. Our strategy identifies molecular fragments predicted to target multiple MMP-2 binding pockets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.